Job ID = 9025649 sra ファイルのダウンロード中... Completed: 150667K bytes transferred in 4 seconds (252649K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 7663 0 7663 0 0 980 0 --:--:-- 0:00:07 --:--:-- 6105 100 30318 0 30318 0 0 3439 0 --:--:-- 0:00:08 --:--:-- 13468 100 47931 0 47931 0 0 5057 0 --:--:-- 0:00:09 --:--:-- 16448 sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 6518497 spots for /home/okishinya/chipatlas/results/ce10/SRX2144175/SRR4188779.sra Written 6518497 spots total rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:00 6518497 reads; of these: 6518497 (100.00%) were unpaired; of these: 679378 (10.42%) aligned 0 times 4543667 (69.70%) aligned exactly 1 time 1295452 (19.87%) aligned >1 times 89.58% overall alignment rate Time searching: 00:02:00 Overall time: 00:02:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 417551 / 5839119 = 0.0715 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sat, 03 Jun 2017 04:50:18: # Command line: callpeak -t SRX2144175.bam -f BAM -g ce -n SRX2144175.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2144175.10 # format = BAM # ChIP-seq file = ['SRX2144175.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Sat, 03 Jun 2017 04:50:18: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:50:18: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:50:18: # Command line: callpeak -t SRX2144175.bam -f BAM -g ce -n SRX2144175.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2144175.20 # format = BAM # ChIP-seq file = ['SRX2144175.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Sat, 03 Jun 2017 04:50:18: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:50:18: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:50:18: # Command line: callpeak -t SRX2144175.bam -f BAM -g ce -n SRX2144175.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2144175.05 # format = BAM # ChIP-seq file = ['SRX2144175.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Sat, 03 Jun 2017 04:50:18: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:50:18: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:50:24: 1000000 INFO @ Sat, 03 Jun 2017 04:50:24: 1000000 INFO @ Sat, 03 Jun 2017 04:50:24: 1000000 INFO @ Sat, 03 Jun 2017 04:50:30: 2000000 INFO @ Sat, 03 Jun 2017 04:50:31: 2000000 INFO @ Sat, 03 Jun 2017 04:50:31: 2000000 INFO @ Sat, 03 Jun 2017 04:50:36: 3000000 INFO @ Sat, 03 Jun 2017 04:50:37: 3000000 INFO @ Sat, 03 Jun 2017 04:50:37: 3000000 INFO @ Sat, 03 Jun 2017 04:50:41: 4000000 INFO @ Sat, 03 Jun 2017 04:50:43: 4000000 INFO @ Sat, 03 Jun 2017 04:50:43: 4000000 INFO @ Sat, 03 Jun 2017 04:50:47: 5000000 INFO @ Sat, 03 Jun 2017 04:50:49: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:50:49: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:50:49: #1 total tags in treatment: 5421568 INFO @ Sat, 03 Jun 2017 04:50:49: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:50:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:50:50: 5000000 INFO @ Sat, 03 Jun 2017 04:50:50: 5000000 INFO @ Sat, 03 Jun 2017 04:50:50: #1 tags after filtering in treatment: 5420618 INFO @ Sat, 03 Jun 2017 04:50:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:50:50: #1 finished! INFO @ Sat, 03 Jun 2017 04:50:50: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:50:51: #2 number of paired peaks: 457 WARNING @ Sat, 03 Jun 2017 04:50:51: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Sat, 03 Jun 2017 04:50:51: start model_add_line... INFO @ Sat, 03 Jun 2017 04:50:52: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:50:52: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:50:52: #1 total tags in treatment: 5421568 INFO @ Sat, 03 Jun 2017 04:50:52: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:50:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:50:52: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:50:52: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:50:52: #1 total tags in treatment: 5421568 INFO @ Sat, 03 Jun 2017 04:50:52: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:50:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:50:53: #1 tags after filtering in treatment: 5420618 INFO @ Sat, 03 Jun 2017 04:50:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:50:53: #1 finished! INFO @ Sat, 03 Jun 2017 04:50:53: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:50:53: #1 tags after filtering in treatment: 5420618 INFO @ Sat, 03 Jun 2017 04:50:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:50:53: #1 finished! INFO @ Sat, 03 Jun 2017 04:50:53: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:50:54: #2 number of paired peaks: 457 WARNING @ Sat, 03 Jun 2017 04:50:54: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Sat, 03 Jun 2017 04:50:54: start model_add_line... INFO @ Sat, 03 Jun 2017 04:50:54: #2 number of paired peaks: 457 WARNING @ Sat, 03 Jun 2017 04:50:54: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Sat, 03 Jun 2017 04:50:54: start model_add_line... INFO @ Sat, 03 Jun 2017 04:50:56: start X-correlation... INFO @ Sat, 03 Jun 2017 04:50:56: end of X-cor INFO @ Sat, 03 Jun 2017 04:50:56: #2 finished! INFO @ Sat, 03 Jun 2017 04:50:56: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 04:50:56: #2 alternative fragment length(s) may be 4,49 bps INFO @ Sat, 03 Jun 2017 04:50:56: #2.2 Generate R script for model : SRX2144175.20_model.r WARNING @ Sat, 03 Jun 2017 04:50:56: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:50:56: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Sat, 03 Jun 2017 04:50:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 04:50:56: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:50:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:50:58: start X-correlation... INFO @ Sat, 03 Jun 2017 04:50:58: end of X-cor INFO @ Sat, 03 Jun 2017 04:50:58: #2 finished! INFO @ Sat, 03 Jun 2017 04:50:58: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 04:50:58: #2 alternative fragment length(s) may be 4,49 bps INFO @ Sat, 03 Jun 2017 04:50:58: #2.2 Generate R script for model : SRX2144175.10_model.r WARNING @ Sat, 03 Jun 2017 04:50:58: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:50:58: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Sat, 03 Jun 2017 04:50:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 04:50:58: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:50:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:50:58: start X-correlation... INFO @ Sat, 03 Jun 2017 04:50:58: end of X-cor INFO @ Sat, 03 Jun 2017 04:50:58: #2 finished! INFO @ Sat, 03 Jun 2017 04:50:58: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 04:50:58: #2 alternative fragment length(s) may be 4,49 bps INFO @ Sat, 03 Jun 2017 04:50:58: #2.2 Generate R script for model : SRX2144175.05_model.r WARNING @ Sat, 03 Jun 2017 04:50:58: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:50:58: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Sat, 03 Jun 2017 04:50:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 04:50:58: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:50:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:51:26: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:51:28: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:51:28: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:51:49: #4 Write output xls file... SRX2144175.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:51:49: #4 Write peak in narrowPeak format file... SRX2144175.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:51:49: #4 Write summits bed file... SRX2144175.05_summits.bed INFO @ Sat, 03 Jun 2017 04:51:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (565 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:51:49: #4 Write output xls file... SRX2144175.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:51:49: #4 Write peak in narrowPeak format file... SRX2144175.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:51:49: #4 Write summits bed file... SRX2144175.10_summits.bed INFO @ Sat, 03 Jun 2017 04:51:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (352 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:51:50: #4 Write output xls file... SRX2144175.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:51:50: #4 Write peak in narrowPeak format file... SRX2144175.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:51:50: #4 Write summits bed file... SRX2144175.20_summits.bed INFO @ Sat, 03 Jun 2017 04:51:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (151 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。